fread.bed: Load bed file as GRanges

In JokingHero/ORFik: Open Reading Frames in Genomics

Load bed file as GRanges

Description

Wraps around import.bed and tries to speed up loading with the use of data.table. Supports gzip, gz, bgz and bed formats. Also safer chromosome naming with the argument chrStyle

Usage

fread.bed(filePath, chrStyle = NULL)

Arguments

filePath	The location of the bed file
chrStyle	a GRanges object, TxDb, FaFile, , a seqlevelsStyle or Seqinfo. (Default: NULL) to get seqlevelsStyle from. In addition if it is a Seqinfo object, seqinfo will be updated. Example of seqlevelsStyle update: Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

Value

a GRanges object

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.bigWig(), export.fstwig(), export.wiggle(), fimport(), findFa(), optimizeReads(), readBam(), readBigWig(), readWig()

Examples

# path to example CageSeq data from hg19 heart sample
cageData <- system.file("extdata", "cage-seq-heart.bed.bgz",
                        package = "ORFik")
fread.bed(cageData)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.